PDB Short entry for 2COR HEADER STRUCTURAL PROTEIN 18-MAY-05 2COR TITLE SOLUTION STRUCTURE OF THE THIRD LIM DOMAIN OF PARTICULARLY INTERESTING TITLE 2 NEW CYS-HIS PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PINCH PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIM DOMAIN; COMPND 5 SYNONYM: PARTICULARLY INTERESTING NEW CYS-HIS PROTEIN, LIM AND COMPND 6 SENESCENT CELL ANTIGEN-LIKE DOMAINS 1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: LIMS1; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P040727-07; SOURCE 8 OTHER_DETAILS: CELL FREE PROTEIN SYNTHESIS KEYWDS LIM DOMAIN, PINCH PROTEIN, PARTICULARLY INTERESTING NEW CYS-HIS KEYWDS 2 PROTEIN, LIM AND SENESCENT CELL ANTIGEN-LIKE DOMAINS 1, STRUCTURAL KEYWDS 3 GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND KEYWDS 4 FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 5 INITIATIVE, RSGI, STRUCTURAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR X.R.QIN,T.NAGASHIMA,F.HAYASHI,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2COR 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2COR 1 VERSN REVDAT 1 18-NOV-05 2COR 0 JRNL AUTH X.R.QIN,T.NAGASHIMA,F.HAYASHI,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE THIRD LIM DOMAIN OF PARTICULARLY JRNL TITL 2 INTERESTING NEW CYS-HIS PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, CYANA 2.0.17 REMARK 3 AUTHORS : VARIAN (VNMR), GUNTERT,P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2COR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000024459. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.39MM 13C, 15N-LABELED PROTEIN; REMARK 210 20MM D-TRIS-HCL; 100MM NACL; 1MM REMARK 210 D-DTT; 0.02% NAN3; 0.05MM ZNCL2 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9296, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION, STRUCTURES WITH REMARK 210 THE LOWEST ENERGY, STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: SPECTROMETER_ID 1 FOR 3D_15N_SEPARATED_NOESY, REMARK 210 SPECTROMETER_ID 2 FOR 3D_13C_SEPARATED_NOESY REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 ILE A 24 145.45 -36.31 REMARK 500 1 ILE A 25 71.25 -115.08 REMARK 500 1 CYS A 44 163.49 -48.24 REMARK 500 1 LEU A 51 178.57 -54.50 REMARK 500 2 PRO A 39 2.87 -69.73 REMARK 500 2 CYS A 44 158.90 -47.63 REMARK 500 2 VAL A 73 39.18 -82.12 REMARK 500 3 SER A 2 140.13 -170.30 REMARK 500 3 SER A 5 41.66 35.73 REMARK 500 3 ALA A 10 133.34 -172.86 REMARK 500 3 LYS A 20 -51.95 -130.49 REMARK 500 3 PRO A 39 2.97 -69.73 REMARK 500 3 LEU A 51 174.66 -54.67 REMARK 500 3 ALA A 55 176.25 -47.72 REMARK 500 4 SER A 3 138.22 -171.85 REMARK 500 4 LYS A 20 -51.90 -129.07 REMARK 500 4 ASP A 26 -70.36 -50.17 REMARK 500 4 PRO A 39 1.35 -69.81 REMARK 500 4 CYS A 44 156.02 -47.90 REMARK 500 4 LEU A 51 171.02 -51.65 REMARK 500 4 ALA A 55 151.44 -35.63 REMARK 500 4 SER A 77 98.89 -63.95 REMARK 500 5 LYS A 9 43.79 -84.11 REMARK 500 5 ILE A 24 148.99 -38.10 REMARK 500 5 ILE A 25 72.31 -118.66 REMARK 500 5 PRO A 39 2.48 -69.74 REMARK 500 5 LEU A 51 175.05 -57.69 REMARK 500 5 VAL A 73 155.78 -41.43 REMARK 500 5 SER A 74 99.18 -44.48 REMARK 500 6 LYS A 20 -54.39 -126.31 REMARK 500 6 PHE A 32 118.43 -165.71 REMARK 500 6 PRO A 39 2.79 -69.78 REMARK 500 6 CYS A 44 153.88 -46.81 REMARK 500 6 LEU A 51 174.41 -48.81 REMARK 500 6 HIS A 68 -35.86 -37.75 REMARK 500 6 SER A 78 135.06 -36.92 REMARK 500 7 ALA A 10 111.96 -169.88 REMARK 500 7 LYS A 20 -52.61 -120.20 REMARK 500 7 ASN A 34 47.91 70.59 REMARK 500 7 PRO A 39 1.00 -69.76 REMARK 500 7 CYS A 44 160.63 -45.95 REMARK 500 7 LEU A 51 173.46 -50.17 REMARK 500 8 SER A 2 113.67 -167.48 REMARK 500 8 LEU A 13 107.15 -51.03 REMARK 500 8 LYS A 20 -50.33 -128.16 REMARK 500 8 PHE A 32 113.04 -162.00 REMARK 500 8 PRO A 39 3.18 -69.79 REMARK 500 8 CYS A 44 163.60 -49.23 REMARK 500 8 LEU A 51 175.36 -49.69 REMARK 500 8 ALA A 55 150.24 -42.36 REMARK 500 REMARK 500 THIS ENTRY HAS 127 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 18 SG REMARK 620 2 CYS A 21 SG 111.9 REMARK 620 3 HIS A 38 ND1 96.4 94.5 REMARK 620 4 HIS A 41 NE2 130.3 104.7 113.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 44 SG REMARK 620 2 CYS A 47 SG 101.2 REMARK 620 3 CYS A 64 SG 116.2 117.9 REMARK 620 4 CYS A 67 SG 103.5 101.4 114.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSS001001107.1 RELATED DB: TARGETDB DBREF 2COR A 8 73 UNP P48059 PINC_HUMAN 125 190 SEQADV 2COR GLY A 1 UNP P48059 CLONING ARTIFACT SEQADV 2COR SER A 2 UNP P48059 CLONING ARTIFACT SEQADV 2COR SER A 3 UNP P48059 CLONING ARTIFACT SEQADV 2COR GLY A 4 UNP P48059 CLONING ARTIFACT SEQADV 2COR SER A 5 UNP P48059 CLONING ARTIFACT SEQADV 2COR SER A 6 UNP P48059 CLONING ARTIFACT SEQADV 2COR GLY A 7 UNP P48059 CLONING ARTIFACT SEQADV 2COR SER A 74 UNP P48059 CLONING ARTIFACT SEQADV 2COR GLY A 75 UNP P48059 CLONING ARTIFACT SEQADV 2COR PRO A 76 UNP P48059 CLONING ARTIFACT SEQADV 2COR SER A 77 UNP P48059 CLONING ARTIFACT SEQADV 2COR SER A 78 UNP P48059 CLONING ARTIFACT SEQADV 2COR GLY A 79 UNP P48059 CLONING ARTIFACT SEQRES 1 A 79 GLY SER SER GLY SER SER GLY GLU LYS ALA ARG GLY LEU SEQRES 2 A 79 GLY LYS TYR ILE CYS GLN LYS CYS HIS ALA ILE ILE ASP SEQRES 3 A 79 GLU GLN PRO LEU ILE PHE LYS ASN ASP PRO TYR HIS PRO SEQRES 4 A 79 ASP HIS PHE ASN CYS ALA ASN CYS GLY LYS GLU LEU THR SEQRES 5 A 79 ALA ASP ALA ARG GLU LEU LYS GLY GLU LEU TYR CYS LEU SEQRES 6 A 79 PRO CYS HIS ASP LYS MET GLY VAL SER GLY PRO SER SER SEQRES 7 A 79 GLY HET ZN A 201 1 HET ZN A 401 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 CYS A 64 LYS A 70 1 7 SHEET 1 A 6 ILE A 24 ILE A 25 0 SHEET 2 A 6 TYR A 16 ILE A 17 -1 SHEET 3 A 6 PRO A 36 TYR A 37 1 SHEET 4 A 6 LEU A 30 ILE A 31 1 SHEET 5 A 6 ARG A 56 LEU A 58 1 SHEET 6 A 6 GLU A 61 TYR A 63 -1 O TYR A 63 N ARG A 56 LINK SG CYS A 18 ZN ZN A 201 1555 1555 2.33 LINK SG CYS A 21 ZN ZN A 201 1555 1555 2.36 LINK ND1 HIS A 38 ZN ZN A 201 1555 1555 2.07 LINK NE2 HIS A 41 ZN ZN A 201 1555 1555 2.06 LINK SG CYS A 44 ZN ZN A 401 1555 1555 2.37 LINK SG CYS A 47 ZN ZN A 401 1555 1555 2.33 LINK SG CYS A 64 ZN ZN A 401 1555 1555 2.34 LINK SG CYS A 67 ZN ZN A 401 1555 1555 2.37 SITE 1 AC1 4 CYS A 18 CYS A 21 HIS A 38 HIS A 41 SITE 1 AC2 4 CYS A 44 CYS A 47 CYS A 64 CYS A 67 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000